Contacts of the helix formed by residues 226 - 241 (chain B) in PDB entry 3IH9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B VAL* 3.6 26.7 - - + -
214B GLY 4.0 0.2 - - - -
223B ARG* 4.2 7.4 - - - +
225B LEU* 1.3 91.2 - - + +
227B SER* 1.3 66.5 + - - +
228B ILE* 4.2 11.7 - - + -
229B VAL* 3.0 30.0 + - + -
230B ALA* 3.1 10.9 + - - +
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLY* 3.0 28.7 + - - -
223B ARG* 3.5 17.2 - - - +
226B PRO* 1.3 70.8 - - - +
228B ILE* 1.3 59.0 + - - +
230B ALA* 3.4 1.6 + - - +
231B ARG* 2.9 30.4 + - - +
336B ARG* 6.0 4.3 - - - -
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 3.8 23.9 - - + -
226B PRO* 3.0 14.5 + - + -
227B SER* 1.3 81.4 + - - +
229B VAL* 1.3 69.9 + - + +
231B ARG* 3.3 45.6 + - - +
232B ARG* 3.3 21.3 + - - +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 3.7 38.8 - - + +
75B LEU* 4.2 13.5 - - + +
76B VAL* 3.7 25.1 - - + +
80B PHE* 4.0 24.0 - - + -
225B LEU* 4.7 4.0 - - + -
226B PRO* 3.0 25.4 + - + +
228B ILE* 1.3 80.6 - - + +
230B ALA* 1.3 67.9 + - - +
232B ARG* 3.5 3.8 + - - +
233B VAL* 3.1 20.3 + - - +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 4.3 14.6 - - + +
214B GLY* 3.8 26.5 - - - -
215B GLY* 4.0 6.5 - - - +
225B LEU* 4.6 12.6 - - + -
226B PRO 3.1 11.1 + - - +
227B SER 3.7 7.0 - - - +
229B VAL* 1.3 77.4 - - - +
231B ARG* 1.3 66.4 + - - +
233B VAL* 3.0 8.8 + - - +
234B VAL* 3.0 26.9 + - - +
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 6.2 1.2 - - - -
214B GLY* 5.7 0.4 - - - -
227B SER 2.9 18.3 + - - +
228B ILE* 3.3 36.6 + - - +
230B ALA* 1.3 76.5 - - - +
232B ARG* 1.3 64.3 + - - +
234B VAL* 3.4 5.4 + - - +
235B SER* 2.8 34.1 + - - +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.0 31.5 + - + +
75B LEU* 4.3 8.3 - - + +
80B PHE* 3.3 40.6 - - + -
84B ASP* 3.2 26.9 + - - -
89B LEU* 3.6 34.1 - - - +
228B ILE 3.3 10.5 + - - +
229B VAL 3.7 7.6 - - - +
230B ALA 3.1 0.4 - - - -
231B ARG* 1.3 84.5 - - - +
233B VAL* 1.3 62.5 + - - +
235B SER* 3.0 20.3 + - - -
236B VAL* 3.0 19.1 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO* 3.3 49.1 - - + +
71B TYR* 4.1 18.1 - - + -
72B ALA* 3.8 24.0 - - + +
75B LEU* 4.2 3.4 - - + -
112B MET* 5.4 0.7 - - - +
211B LEU* 4.3 18.8 - - + -
229B VAL 3.1 14.8 + - - +
230B ALA* 3.0 10.4 + - - +
232B ARG* 1.3 75.8 - - - +
234B VAL* 1.3 62.7 + - - +
236B VAL* 3.5 3.1 + - - +
237B MET* 3.1 22.6 + - + +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.7 42.2 - - + +
230B ALA 3.0 17.9 + - - +
231B ARG* 3.9 5.4 - - - +
233B VAL* 1.3 74.1 - - - +
235B SER* 1.3 60.4 + - - +
237B MET* 3.1 7.3 + - - +
238B THR* 2.9 33.9 + - - +
256B PRO* 3.6 30.7 - - + -
268B ALA* 4.0 11.9 - - + +
270B PRO* 4.0 19.1 - - + -
306B LEU* 5.8 0.2 - - + -
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ARG* 2.8 26.7 + - - +
232B ARG* 3.0 17.4 + - - -
234B VAL* 1.3 76.7 - - - +
236B VAL* 1.3 58.8 + - - +
238B THR* 3.2 9.0 + - - -
239B SER* 3.0 28.6 + - - -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 4.1 15.3 - - + -
89B LEU* 3.7 35.9 - - + +
110B ASN* 4.3 19.1 - - + +
111B ALA 4.5 2.9 - - - +
112B MET* 3.7 28.1 - - + +
232B ARG* 3.0 18.7 + - - +
233B VAL 4.0 3.6 - - - +
235B SER* 1.3 76.0 - - - +
237B MET* 1.3 59.8 + - - +
239B SER* 3.7 9.0 - - - +
240B SER* 2.9 25.0 + - - +
241B GLY 3.4 3.8 + - - -
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Residues in contact with MET 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO* 4.1 18.2 - - + -
112B MET* 4.5 9.9 - - - -
211B LEU* 4.1 24.2 - - - -
233B VAL 3.1 17.9 + - - +
234B VAL* 3.1 14.8 + - - +
236B VAL* 1.3 75.0 - - - +
238B THR* 1.3 61.6 + - - +
241B GLY* 2.8 33.1 + - - +
242B MET 4.4 0.5 + - - -
256B PRO* 4.0 11.4 - - + +
257B ALA* 3.5 42.9 + - - +
258B LYS* 3.8 4.7 - - + +
266B LEU* 3.5 28.3 - - + +
268B ALA* 4.7 9.9 - - + -
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B VAL* 2.9 17.3 + - - +
235B SER* 3.2 10.9 + - - -
237B MET* 1.3 79.9 - - - +
239B SER* 1.3 62.9 + - - +
241B GLY 4.6 0.3 + - - -
242B MET 5.3 0.9 + - - -
246B ALA* 4.1 16.3 - - - +
249B TRP* 5.4 6.9 - - - -
250B LEU* 4.2 23.0 - - + +
255B ILE 6.2 0.2 - - - -
256B PRO* 3.1 29.1 - - + +
306B LEU* 4.1 22.4 - - + +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU 4.6 8.3 + - - -
91B PRO* 3.3 24.7 - - - +
235B SER 3.0 16.3 + - - -
236B VAL* 3.7 8.8 - - - +
238B THR* 1.3 79.5 - - - +
240B SER* 1.3 69.7 + - - +
246B ALA* 3.2 19.9 - - - +
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Residues in contact with SER 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU 4.8 1.2 + - - -
90B ASN 4.1 0.7 - - - -
91B PRO* 3.3 23.3 - - - +
92B SER 4.9 1.6 - - - -
110B ASN* 3.1 37.8 + - - +
112B MET* 3.8 8.9 - - - +
113B ILE* 5.5 0.2 - - - +
236B VAL* 2.9 12.4 + - - +
239B SER* 1.3 88.0 + - - +
241B GLY* 1.3 68.7 + - - +
242B MET 3.2 2.7 - - - -
243B TYR* 3.0 22.5 + - - +
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Residues in contact with GLY 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B MET* 4.2 5.2 - - - -
236B VAL 3.4 2.8 + - - -
237B MET* 2.8 23.5 + - - -
239B SER 3.9 0.2 - - - -
240B SER* 1.3 76.3 - - - +
242B MET* 1.3 73.0 + - - +
243B TYR* 3.6 8.1 + - - -
257B ALA 3.7 10.5 - - - -
258B LYS* 3.4 27.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il